Manganese in PDB 1wao: PP5 Structure
Enzymatic activity of PP5 Structure
All present enzymatic activity of PP5 Structure:
3.1.3.16;
Protein crystallography data
The structure of PP5 Structure, PDB code: 1wao
was solved by
D.Barford,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
33.78 /
2.9
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.740,
117.540,
200.410,
90.00,
93.79,
90.00
|
|
R / Rfree (%)
|
24.7 /
29
|
Manganese Binding Sites:
The binding sites of Manganese atom in the PP5 Structure
(pdb code 1wao). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
PP5 Structure, PDB code: 1wao:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 1 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mn601
b:85.4
occ:1.00
|
OD1
|
1:ASN303
|
2.2
|
61.9
|
1.0
|
|
NE2
|
1:HIS352
|
2.4
|
42.7
|
1.0
|
|
ND1
|
1:HIS427
|
2.6
|
58.7
|
1.0
|
|
OD2
|
1:ASP271
|
2.7
|
52.8
|
1.0
|
|
CG
|
1:ASN303
|
3.0
|
62.5
|
1.0
|
|
CE1
|
1:HIS352
|
3.2
|
45.2
|
1.0
|
|
ND2
|
1:ASN303
|
3.2
|
62.0
|
1.0
|
|
CE1
|
1:HIS427
|
3.2
|
58.4
|
1.0
|
|
CG
|
1:ASP271
|
3.5
|
53.1
|
1.0
|
|
CD2
|
1:HIS352
|
3.5
|
48.3
|
1.0
|
|
CG
|
1:HIS427
|
3.6
|
54.8
|
1.0
|
|
MN
|
1:MN602
|
3.6
|
0.1
|
1.0
|
|
OD1
|
1:ASP271
|
3.7
|
53.1
|
1.0
|
|
OD2
|
1:ASP242
|
3.7
|
55.6
|
1.0
|
|
CA
|
1:HIS427
|
3.7
|
48.0
|
1.0
|
|
O
|
1:HIS427
|
3.9
|
44.0
|
1.0
|
|
CB
|
1:HIS427
|
4.1
|
52.0
|
1.0
|
|
CD2
|
1:HIS304
|
4.2
|
57.0
|
1.0
|
|
C
|
1:HIS427
|
4.3
|
45.7
|
1.0
|
|
NE2
|
1:HIS427
|
4.3
|
58.3
|
1.0
|
|
ND1
|
1:HIS352
|
4.4
|
45.8
|
1.0
|
|
CD2
|
1:HIS427
|
4.5
|
56.4
|
1.0
|
|
CB
|
1:ASN303
|
4.5
|
59.5
|
1.0
|
|
CG
|
1:HIS352
|
4.6
|
47.1
|
1.0
|
|
N
|
1:HIS427
|
4.7
|
46.6
|
1.0
|
|
CB
|
1:ASP271
|
4.7
|
50.7
|
1.0
|
|
N
|
1:ASN303
|
4.8
|
55.2
|
1.0
|
|
NE2
|
1:HIS304
|
4.8
|
57.1
|
1.0
|
|
CG
|
1:ASP242
|
4.9
|
53.5
|
1.0
|
|
O
|
1:LEU385
|
5.0
|
59.3
|
1.0
|
|
Manganese binding site 2 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 2 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mn602
b:0.1
occ:1.00
|
NE2
|
1:HIS244
|
2.1
|
55.2
|
1.0
|
|
OD2
|
1:ASP271
|
2.8
|
52.8
|
1.0
|
|
OD2
|
1:ASP242
|
2.9
|
55.6
|
1.0
|
|
CE1
|
1:HIS244
|
3.1
|
52.2
|
1.0
|
|
CD2
|
1:HIS244
|
3.1
|
52.4
|
1.0
|
|
OH
|
1:TYR451
|
3.4
|
46.4
|
1.0
|
|
MN
|
1:MN601
|
3.6
|
85.4
|
1.0
|
|
CG
|
1:ASP242
|
3.9
|
53.5
|
1.0
|
|
NH1
|
1:ARG275
|
4.0
|
75.0
|
1.0
|
|
CG
|
1:ASP271
|
4.0
|
53.1
|
1.0
|
|
OE1
|
1:GLU76
|
4.2
|
76.3
|
1.0
|
|
CZ
|
1:TYR451
|
4.2
|
46.2
|
1.0
|
|
ND1
|
1:HIS244
|
4.2
|
51.7
|
1.0
|
|
CG
|
1:HIS244
|
4.3
|
52.5
|
1.0
|
|
CD2
|
1:HIS304
|
4.4
|
57.0
|
1.0
|
|
CB
|
1:ASP242
|
4.4
|
50.5
|
1.0
|
|
NE2
|
1:HIS304
|
4.5
|
57.1
|
1.0
|
|
CE1
|
1:PHE446
|
4.6
|
46.0
|
1.0
|
|
O
|
1:HIS427
|
4.6
|
44.0
|
1.0
|
|
CE2
|
1:TYR451
|
4.6
|
44.6
|
1.0
|
|
CB
|
1:ASP271
|
4.7
|
50.7
|
1.0
|
|
CZ
|
1:PHE446
|
4.9
|
43.6
|
1.0
|
|
OD1
|
1:ASP242
|
4.9
|
54.1
|
1.0
|
|
OD1
|
1:ASP271
|
5.0
|
53.1
|
1.0
|
|
Manganese binding site 3 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 3 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mn601
b:0.1
occ:1.00
|
NE2
|
2:HIS352
|
2.2
|
87.7
|
1.0
|
|
OD1
|
2:ASN303
|
2.4
|
0.7
|
1.0
|
|
OD2
|
2:ASP271
|
2.6
|
92.1
|
1.0
|
|
ND1
|
2:HIS427
|
2.6
|
72.1
|
1.0
|
|
MN
|
2:MN602
|
2.7
|
0.3
|
1.0
|
|
CE1
|
2:HIS352
|
2.9
|
87.9
|
1.0
|
|
CG
|
2:ASP271
|
3.2
|
92.5
|
1.0
|
|
CG
|
2:ASN303
|
3.3
|
0.6
|
1.0
|
|
CE1
|
2:HIS427
|
3.3
|
71.3
|
1.0
|
|
OD1
|
2:ASP271
|
3.4
|
93.1
|
1.0
|
|
CD2
|
2:HIS352
|
3.4
|
87.9
|
1.0
|
|
OD2
|
2:ASP242
|
3.5
|
88.6
|
1.0
|
|
CA
|
2:HIS427
|
3.6
|
70.9
|
1.0
|
|
ND2
|
2:ASN303
|
3.6
|
0.4
|
1.0
|
|
CG
|
2:HIS427
|
3.6
|
72.1
|
1.0
|
|
O
|
2:HIS427
|
3.8
|
69.5
|
1.0
|
|
CB
|
2:HIS427
|
4.1
|
71.7
|
1.0
|
|
C
|
2:HIS427
|
4.1
|
70.2
|
1.0
|
|
ND1
|
2:HIS352
|
4.1
|
89.0
|
1.0
|
|
CD2
|
2:HIS304
|
4.2
|
99.8
|
1.0
|
|
CG
|
2:HIS352
|
4.4
|
88.2
|
1.0
|
|
CB
|
2:ASP271
|
4.5
|
92.0
|
1.0
|
|
NE2
|
2:HIS427
|
4.5
|
71.7
|
1.0
|
|
N
|
2:HIS427
|
4.5
|
70.1
|
1.0
|
|
CG
|
2:ASP242
|
4.6
|
87.7
|
1.0
|
|
CD2
|
2:HIS427
|
4.6
|
72.2
|
1.0
|
|
CB
|
2:ASN303
|
4.7
|
0.5
|
1.0
|
|
OD1
|
2:ASP242
|
4.9
|
89.1
|
1.0
|
|
NE2
|
2:HIS244
|
4.9
|
79.9
|
1.0
|
|
N
|
2:ASN303
|
4.9
|
0.3
|
1.0
|
|
NE2
|
2:HIS304
|
4.9
|
99.7
|
1.0
|
|
Manganese binding site 4 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 4 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mn602
b:0.3
occ:1.00
|
OD2
|
2:ASP271
|
2.4
|
92.1
|
1.0
|
|
NE2
|
2:HIS244
|
2.6
|
79.9
|
1.0
|
|
MN
|
2:MN601
|
2.7
|
0.1
|
1.0
|
|
OD2
|
2:ASP242
|
2.7
|
88.6
|
1.0
|
|
CE1
|
2:HIS244
|
3.4
|
78.5
|
1.0
|
|
CG
|
2:ASP271
|
3.7
|
92.5
|
1.0
|
|
CD2
|
2:HIS244
|
3.8
|
81.0
|
1.0
|
|
CG
|
2:ASP242
|
3.9
|
87.7
|
1.0
|
|
CD2
|
2:HIS304
|
4.0
|
99.8
|
1.0
|
|
O
|
2:HIS427
|
4.0
|
69.5
|
1.0
|
|
OH
|
2:TYR451
|
4.1
|
84.3
|
1.0
|
|
NH1
|
2:ARG275
|
4.2
|
89.9
|
1.0
|
|
NE2
|
2:HIS304
|
4.2
|
99.7
|
1.0
|
|
OE1
|
2:GLU76
|
4.4
|
81.6
|
1.0
|
|
OD1
|
2:ASP271
|
4.5
|
93.1
|
1.0
|
|
CB
|
2:ASP271
|
4.5
|
92.0
|
1.0
|
|
NE2
|
2:HIS352
|
4.5
|
87.7
|
1.0
|
|
OD1
|
2:ASN303
|
4.6
|
0.7
|
1.0
|
|
C
|
2:HIS427
|
4.6
|
70.2
|
1.0
|
|
ND1
|
2:HIS244
|
4.6
|
79.8
|
1.0
|
|
CE1
|
2:HIS352
|
4.6
|
87.9
|
1.0
|
|
CB
|
2:ASP242
|
4.7
|
86.8
|
1.0
|
|
CA
|
2:HIS427
|
4.7
|
70.9
|
1.0
|
|
OD1
|
2:ASP242
|
4.8
|
89.1
|
1.0
|
|
CG
|
2:HIS244
|
4.8
|
80.9
|
1.0
|
|
ND1
|
2:HIS427
|
4.9
|
72.1
|
1.0
|
|
CE1
|
2:PHE446
|
5.0
|
66.2
|
1.0
|
|
CZ
|
2:TYR451
|
5.0
|
84.1
|
1.0
|
|
Manganese binding site 5 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 5 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Mn601
b:0.7
occ:1.00
|
NE2
|
3:HIS352
|
2.6
|
0.2
|
1.0
|
|
OD2
|
3:ASP271
|
2.6
|
91.1
|
1.0
|
|
MN
|
3:MN602
|
2.7
|
0.2
|
1.0
|
|
OD1
|
3:ASN303
|
2.7
|
0.9
|
1.0
|
|
ND1
|
3:HIS427
|
2.7
|
97.0
|
1.0
|
|
CE1
|
3:HIS352
|
3.2
|
0.4
|
1.0
|
|
CG
|
3:ASP271
|
3.3
|
93.0
|
1.0
|
|
OD2
|
3:ASP242
|
3.4
|
89.4
|
1.0
|
|
CE1
|
3:HIS427
|
3.4
|
96.8
|
1.0
|
|
CG
|
3:ASN303
|
3.5
|
0.9
|
1.0
|
|
OD1
|
3:ASP271
|
3.5
|
93.3
|
1.0
|
|
CA
|
3:HIS427
|
3.6
|
92.7
|
1.0
|
|
CG
|
3:HIS427
|
3.7
|
96.3
|
1.0
|
|
ND2
|
3:ASN303
|
3.7
|
0.3
|
1.0
|
|
O
|
3:HIS427
|
3.7
|
90.8
|
1.0
|
|
CD2
|
3:HIS352
|
3.8
|
0.7
|
1.0
|
|
C
|
3:HIS427
|
4.1
|
91.6
|
1.0
|
|
CB
|
3:HIS427
|
4.1
|
94.2
|
1.0
|
|
CD2
|
3:HIS304
|
4.2
|
0.6
|
1.0
|
|
ND1
|
3:HIS352
|
4.4
|
0.2
|
1.0
|
|
CG
|
3:ASP242
|
4.5
|
88.0
|
1.0
|
|
NE2
|
3:HIS427
|
4.5
|
96.4
|
1.0
|
|
N
|
3:HIS427
|
4.6
|
93.0
|
1.0
|
|
CB
|
3:ASP271
|
4.6
|
93.7
|
1.0
|
|
CD2
|
3:HIS427
|
4.6
|
96.8
|
1.0
|
|
NE2
|
3:HIS244
|
4.7
|
88.5
|
1.0
|
|
CG
|
3:HIS352
|
4.7
|
0.9
|
1.0
|
|
NE2
|
3:HIS304
|
4.8
|
0.1
|
1.0
|
|
OD1
|
3:ASP242
|
4.9
|
88.0
|
1.0
|
|
CB
|
3:ASN303
|
4.9
|
0.8
|
1.0
|
|
Manganese binding site 6 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 6 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Mn602
b:0.2
occ:1.00
|
NE2
|
3:HIS244
|
2.4
|
88.5
|
1.0
|
|
OD2
|
3:ASP271
|
2.6
|
91.1
|
1.0
|
|
MN
|
3:MN601
|
2.7
|
0.7
|
1.0
|
|
OD2
|
3:ASP242
|
2.9
|
89.4
|
1.0
|
|
CE1
|
3:HIS244
|
3.1
|
89.2
|
1.0
|
|
CD2
|
3:HIS244
|
3.6
|
87.8
|
1.0
|
|
OH
|
3:TYR451
|
3.6
|
85.7
|
1.0
|
|
CG
|
3:ASP271
|
3.8
|
93.0
|
1.0
|
|
CD2
|
3:HIS304
|
3.9
|
0.6
|
1.0
|
|
NH1
|
3:ARG275
|
3.9
|
0.7
|
1.0
|
|
CG
|
3:ASP242
|
4.1
|
88.0
|
1.0
|
|
NE2
|
3:HIS304
|
4.1
|
0.1
|
1.0
|
|
OE1
|
3:GLU76
|
4.3
|
0.8
|
1.0
|
|
ND1
|
3:HIS244
|
4.4
|
88.0
|
1.0
|
|
O
|
3:HIS427
|
4.4
|
90.8
|
1.0
|
|
CZ
|
3:TYR451
|
4.6
|
86.8
|
1.0
|
|
CB
|
3:ASP271
|
4.6
|
93.7
|
1.0
|
|
CG
|
3:HIS244
|
4.6
|
86.0
|
1.0
|
|
OD1
|
3:ASP271
|
4.7
|
93.3
|
1.0
|
|
OE2
|
3:GLU76
|
4.7
|
0.0
|
1.0
|
|
CB
|
3:ASP242
|
4.8
|
86.7
|
1.0
|
|
OD1
|
3:ASN303
|
4.8
|
0.9
|
1.0
|
|
NE2
|
3:HIS352
|
4.9
|
0.2
|
1.0
|
|
C
|
3:HIS427
|
4.9
|
91.6
|
1.0
|
|
CE1
|
3:HIS352
|
5.0
|
0.4
|
1.0
|
|
CD
|
3:GLU76
|
5.0
|
0.7
|
1.0
|
|
OD1
|
3:ASP242
|
5.0
|
88.0
|
1.0
|
|
Manganese binding site 7 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 7 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Mn601
b:93.1
occ:1.00
|
NE2
|
4:HIS352
|
2.2
|
54.0
|
1.0
|
|
OD1
|
4:ASN303
|
2.4
|
66.8
|
1.0
|
|
ND1
|
4:HIS427
|
2.5
|
63.0
|
1.0
|
|
OD2
|
4:ASP271
|
2.8
|
49.4
|
1.0
|
|
CE1
|
4:HIS352
|
2.8
|
55.8
|
1.0
|
|
MN
|
4:MN602
|
3.0
|
0.4
|
1.0
|
|
CE1
|
4:HIS427
|
3.3
|
61.2
|
1.0
|
|
CD2
|
4:HIS352
|
3.4
|
56.7
|
1.0
|
|
CG
|
4:ASP271
|
3.4
|
55.3
|
1.0
|
|
CG
|
4:ASN303
|
3.4
|
65.0
|
1.0
|
|
CA
|
4:HIS427
|
3.4
|
53.5
|
1.0
|
|
CG
|
4:HIS427
|
3.5
|
61.6
|
1.0
|
|
OD2
|
4:ASP242
|
3.5
|
64.5
|
1.0
|
|
OD1
|
4:ASP271
|
3.6
|
51.8
|
1.0
|
|
ND2
|
4:ASN303
|
3.7
|
65.1
|
1.0
|
|
O
|
4:HIS427
|
3.7
|
56.4
|
1.0
|
|
CB
|
4:HIS427
|
3.8
|
57.8
|
1.0
|
|
C
|
4:HIS427
|
4.0
|
54.4
|
1.0
|
|
ND1
|
4:HIS352
|
4.1
|
57.3
|
1.0
|
|
CG
|
4:HIS352
|
4.3
|
56.6
|
1.0
|
|
N
|
4:HIS427
|
4.4
|
52.4
|
1.0
|
|
NE2
|
4:HIS427
|
4.4
|
61.8
|
1.0
|
|
CD2
|
4:HIS304
|
4.4
|
72.4
|
1.0
|
|
CD2
|
4:HIS427
|
4.5
|
62.4
|
1.0
|
|
CG
|
4:ASP242
|
4.6
|
61.7
|
1.0
|
|
CB
|
4:ASP271
|
4.6
|
58.4
|
1.0
|
|
CB
|
4:ASN303
|
4.7
|
63.9
|
1.0
|
|
OD1
|
4:ASP242
|
4.8
|
61.5
|
1.0
|
|
N
|
4:ASN303
|
4.9
|
62.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 1wao
Go back to
Manganese Binding Sites List in 1wao
Manganese binding site 8 out
of 8 in the PP5 Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of PP5 Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Mn602
b:0.4
occ:1.00
|
OD2
|
4:ASP271
|
2.8
|
49.4
|
1.0
|
|
NE2
|
4:HIS244
|
2.9
|
60.4
|
1.0
|
|
MN
|
4:MN601
|
3.0
|
93.1
|
1.0
|
|
OE1
|
4:GLU76
|
3.3
|
73.6
|
1.0
|
|
CE1
|
4:HIS244
|
3.4
|
58.4
|
1.0
|
|
OD2
|
4:ASP242
|
3.5
|
64.5
|
1.0
|
|
NH1
|
4:ARG275
|
3.7
|
76.3
|
1.0
|
|
CD2
|
4:HIS304
|
3.7
|
72.4
|
1.0
|
|
NE2
|
4:HIS304
|
3.7
|
73.8
|
1.0
|
|
OH
|
4:TYR451
|
3.9
|
54.6
|
1.0
|
|
CG
|
4:ASP271
|
4.0
|
55.3
|
1.0
|
|
CD2
|
4:HIS244
|
4.2
|
58.3
|
1.0
|
|
CD
|
4:GLU76
|
4.2
|
72.6
|
1.0
|
|
O
|
4:HIS427
|
4.3
|
56.4
|
1.0
|
|
OE2
|
4:GLU76
|
4.4
|
70.0
|
1.0
|
|
CG
|
4:ASP242
|
4.6
|
61.7
|
1.0
|
|
OD1
|
4:ASN303
|
4.6
|
66.8
|
1.0
|
|
OD1
|
4:ASP271
|
4.7
|
51.8
|
1.0
|
|
ND1
|
4:HIS244
|
4.7
|
57.0
|
1.0
|
|
ND2
|
4:ASN303
|
4.8
|
65.1
|
1.0
|
|
CZ
|
4:ARG275
|
4.8
|
75.5
|
1.0
|
|
CZ
|
4:TYR451
|
4.9
|
51.1
|
1.0
|
|
CE1
|
4:HIS304
|
4.9
|
74.2
|
1.0
|
|
NE2
|
4:HIS352
|
4.9
|
54.0
|
1.0
|
|
CG
|
4:HIS304
|
4.9
|
71.4
|
1.0
|
|
C
|
4:HIS427
|
4.9
|
54.4
|
1.0
|
|
Reference:
J.Yang,
S.M.Roe,
M.J.Cliff,
M.A.Williams,
J.E.Ladbury,
P.T.Cohen,
D.Barford.
Molecular Basis For Tpr Domain-Mediated Regulation of Protein Phosphatase 5 Embo J. V. 24 1 2005.
ISSN: ISSN 0261-4189
PubMed: 15577939
DOI: 10.1038/SJ.EMBOJ.7600496
Page generated: Sat Oct 5 12:53:16 2024
|
